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. 2017 May 23;8:63.
doi: 10.3389/fgene.2017.00063. eCollection 2017.

An Enhancer's Length and Composition Are Shaped by Its Regulatory Task

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Free PMC article

An Enhancer's Length and Composition Are Shaped by Its Regulatory Task

Lily Li et al. Front Genet. .
Free PMC article

Abstract

Enhancers drive the gene expression patterns required for virtually every process in metazoans. We propose that enhancer length and transcription factor (TF) binding site composition-the number and identity of TF binding sites-reflect the complexity of the enhancer's regulatory task. In development, we define regulatory task complexity as the number of fates specified in a set of cells at once. We hypothesize that enhancers with more complex regulatory tasks will be longer, with more, but less specific, TF binding sites. Larger numbers of binding sites can be arranged in more ways, allowing enhancers to drive many distinct expression patterns, and therefore cell fates, using a finite number of TF inputs. We compare ~100 enhancers patterning the more complex anterior-posterior (AP) axis and the simpler dorsal-ventral (DV) axis in Drosophila and find that the AP enhancers are longer with more, but less specific binding sites than the (DV) enhancers. Using a set of ~3,500 enhancers, we find enhancer length and TF binding site number again increase with increasing regulatory task complexity. Therefore, to be broadly applicable, computational tools to study enhancers must account for differences in regulatory task.

Keywords: Drosophila melanogaster; embryogenesis; enhancer; gene regulation; transcription factor.

Figures

Figure 1
Figure 1
Regulatory task complexity can shape enhancer length and binding site composition. (A) We propose that more complex regulatory tasks, e.g., cell patterning decisions, are associated with longer enhancers with more binding sites. More binding sites can be arranged within an enhancer in more ways, allowing for the specification of a wider variety of expression patterns and, therefore, more complex tasks. (B) We plot the minimum number of TF binding sites required for enhancers of varying lengths to achieve distinguishability from the genomic background. We show the results for three motif hit probabilities, corresponding to the median, first and third quartiles of Drosophila TF binding specificities. As motif hit probability p decreases from ~2 in 1 kb (2 × 10−3) to ~6 in 100 kb (6 × 10−5), an enhancer of the same length requires fewer binding sites to be distinguishable from the background. (C) To test the effect of genome accessibility, we plot the minimum number of TF binding sites required for enhancers of varying length in the context of different accessible genome sizes (N). Varying the accessible regions of the genome has a minor impact on the trend of numbers of TF binding sites increasing with enhancer length.
Figure 2
Figure 2
The more complex AP axis is patterned by enhancers with more TF binding sites. We show the scatterplots and associated boxplots of (A) the length of AP and DV enhancers, (B) the number of TF binding sites predicted in AP and DV enhancers, (C) the number of TF binding sites normalized by the number of TFs involved, (D) the motif hit probability of TFs involved in AP and DV patterning, and (E) the average motif hit probability of AP and DV enhancers. These data are consistent with our hypothesis that enhancers carrying out more complex regulatory tasks will have more binding sites, in this case because AP enhancers are both longer and have lower average TF binding specificity. In all box plots, the boxes indicate the lower and upper quartiles, with the line within the box indicating the median. Whiskers extend to 1.5*IQR (interquartile range) plus or minus the upper and lower quartile, respectively, and the stars indicate outliers that fall outside the whiskers. P-values from Mann-Whitney rank tests are shown.
Figure 3
Figure 3
Decreasing regulatory task complexity over embryogenesis is associated with decreasing enhancer length. We show boxplots of (A) the length of minimal Vienna Tile enhancers, (B) the number of TF binding sites predicted in minimal Vienna Tile enhancers, (C) the number of TF binding sites predicted in minimal Vienna Tile enhancers normalized by TFs concurrently expressed, and (E) the average motif hit probability of minimal Vienna Tile enhancers over developmental stages 4–16. The heatmaps display the Bonferroni-adjusted p-values from the Mann-Whitney rank test between (D) pairwise distributions of Vienna Tile enhancer length and between (F) pairwise distributions of the number of TF binding sites predicted in Vienna Tile enhancers per TFs concurrently expressed. In all box plots, the boxes indicate the lower and upper quartiles, with the line within the box indicating the median. Whiskers extend to 1.5*IQR plus or minus the upper and lower quartile, respectively, and the stars indicate outliers that fall outside the whiskers.

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References

    1. Arnosti D. N., Kulkarni M. M. (2005). Transcriptional enhancers: intelligent enhanceosomes or flexible billboards? J. Cell. Biochem. 94, 890–898. 10.1002/jcb.20352 - DOI - PubMed
    1. Berg O. G., von Hippel P. H. (1987). Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193, 723–50. 10.1016/0022-2836(87)90354-8 - DOI - PubMed
    1. Berman B. P., Nibu Y., Pfeiffer B. D., Tomancak P., Celniker S. E., Levine M., et al. . (2002). Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. U.S.A. 99, 757–762. 10.1073/pnas.231608898 - DOI - PMC - PubMed
    1. Blackwood E. M., Kadonaga J. T. (1998). Going the distance: a current view of enhancer action. Science 281, 60–63. 10.1126/science.281.5373.60 - DOI - PubMed
    1. Ellis L. L., Huang W., Quinn A. M., Ahuja A., Alfrejd B., Gomez F. E., et al. . (2014). Intrapopulation genome size variation in D. Melanogaster reflects life history variation and plasticity. PLoS Genet. 10:4522. 10.1371/journal.pgen.1004522 - DOI - PMC - PubMed

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